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Evolution and genetics of adaption Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

Adaption definition

A

A characteristic that enhances the survival of reproduction of organisms that bear it, relative to alternative states

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2
Q

What does the hardy weinburg equation describe

A

The genetic allele frequency in a population that is not evolving

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3
Q

What does the Hardy weinburg equation predict

A

The genotype and allele frequencies in one generation from the allele frequencies in the previous generation

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4
Q

What are the assumptions of the hardy weinburg equation

A

No selection, no mutation and large population, random mating

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5
Q

What is the hardy weinburg equation

A

p^2 + 2pq+ q^2 = 1

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6
Q

Whats the usefullness of the hardy weinburg equation

A

Gives a null model

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7
Q

What 4 evolutionary forces are needed to disrupt the hardy weinburg equation

A

Random mutations, genetic drift, Migration between species and isolated populations and natural selection

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8
Q

Natural selection definition

A

Differerntial survival and or reproduction of individuals/ any group of reproductive units

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9
Q

How do you work out the fitness of a species

A

Probability of survival x average number of offspring for a class of individuals

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10
Q

Whats the maximum fitness

A

w=1

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11
Q

Whats the selection coefficient

A

The difference between w and 1

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12
Q

How do we know natural selection exists?

A

Correlations between trait and environment, responses to experimental change in the enviornment, coreelations between trait and fitness component, signatures in the genome

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13
Q

What are the problems with detecting selection?

A

Genetic drift can spread traits, ancestral state, selection might not cause any change, selection might not be working at the individual level, linkage

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14
Q

What does natural selection not do?

A

Always lead to adaptation, produce perfection, always progress, produce a balanced, harmonious world, consider ethics

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15
Q

What is the levels of standing genetic variation

A

Presence of alternative forms of a gene and giving lockers of a population

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16
Q

What do the levels of standing genetic variation predict

A

A species ability to adapt

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17
Q

What are some of the processes responsible for generating diversity

A

Mutation, sex, ploidy, balancing selection

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18
Q

What kind of mutations are passed on to the next generation

A

Germ line

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19
Q

What do germ line mutations include

A

Point mutations such as substitution, insertion, deletion and inversion

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20
Q

What mutations do not lead to changes

A

Synonymous and silent

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21
Q

What are some examples of Non-synonymous mutations

A

Missense, nonsense, frame change

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22
Q

Example of inversion mutations

A

Wading birds and their different male morphs: Independence, satellite and faeder

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23
Q

How do beneficial mutations arise?

A

Independent assortment, random fertilisation, crossing over, ploidy, balancing selection

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24
Q

What happens in independant assortment

A

Sexual reproduction mixes the DNA from the two haploid gametes to produce diploid offspring, when chromosomes line up, the chromosomes pull apart

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25
Q

What happens in crossing over

A

Flailing chromosomes exchange genetic material between the chromosome pairs

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26
Q

What happens in ploidy

A

Diploid means two copies of everything, the rarer the recesive allele, the greater the degree of protection from natural protection

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27
Q

What are the two types of balancing selection

A

Heterozygote advantage and frequency dependant selection

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28
Q

What happens in heterozygote advantage and example

A

The heterozygote s fittest over dominance for example sick cell anaemia in Africa is beneficial for patients with malaria so is maintained in the population

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29
Q

What happens in frequency dependant selection and the two type

A

The rare alleles have the highest fitness.
Postivie: fitness of a genotyoe goes up with its frequency- variation isnt maintained
Negative: fitness of genotype goes down as its frequnecy goes up- maintains frequency

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30
Q

Example of frequency dependant selection

A

Cichlid feed by taking mouthfuls of fish of the sides- Controlled by a single gene

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31
Q

Polymorphism definition

A

Differences between individuals of the same species

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32
Q

Divergence definition

A

Differences between individuals of different species

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33
Q

Molecular evolutionary terms

A

Evolution is changes in allele frequencies over time
a chromosome carries one possible allele at any given locus
mutation generates a new allele which can be inherited by its carriers descendants
Each new allele starts as a mutation in a single individual
Frequency of the allele can increase or decrease in each passing generation

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34
Q

What can the starting frequency if the new mutation be calculated with

A

1/(2N) - n is the population of diploid individuals

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35
Q

Who proposed the neutral theory and when

A

Mootoo Kimura in 1968

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36
Q

What does the neutral theory hypothesise

A

The the fate of most mutations contributing to molecular is determined by drift rather than selection

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37
Q

What are the assumptions in the neutral theory

A

The mutations are either neutral or weakly selected

38
Q

How do we measure DNA sequence variation

A

Single nucleotide polymorphisms (SNPS)

39
Q

What does the Wright-Fisher model do

A

It makes explicitly, testable predications about patterns of polymorphism and divergence

40
Q

What are the assumptions of the Wright-fisher model

A

random mating, no selective differences, new individuals are formed by sampling at random with replacement of gametes produced by individuals

41
Q

What is the Wright- fisher model equation

A

E(pi) = 4NeU

42
Q

Whats the importance of the Wright-fisher model

A

Gives us a way of explaining patterns of genetic diversity
We can formally identify patterns of variation and use that to determine selective forces
Species with larger population size and higher mutation rates tend to be more variable

43
Q

What are commonly used neutral markers

A

Synonymous polymorphisms, silent polymorphisms

44
Q

What does Ne stand for

A

effective population size

45
Q

What are the effects of populations bottlenecks on Ne

A

Loss of variability due to genetic drift being more rapid in smaller populations
Populations that experience bottlenecks are expected to have a low Ne

46
Q

What do deleterious variants do

A

Tend to decrease in frequency in the population overtime
tend to segregate at lower frequencies than neutral variants
less likely to get fixed than neutral variants
could linger in the population for a substantial amount of time

47
Q

What do beneficial variants do

A

Tend to increase in frequency in the population
Tend to segregate at higher frequencies than neutral alleles
More likely to get fixed than neutral variants

48
Q

What do small Ne lead to

A

Much weakened selection, leading to deleterious mutations drifting to high frequencies

49
Q

What is it predicted that repeated bottlenecks lead to

A

Deleterious variants being more common in non-African populations

50
Q

What are the mutations in synonymous polymorphisms likely to be

A

Most mutations are probably neutral

51
Q

What are mutations in non- synonymous polymorphisms likely to be

A

They’re likely to influence fitness

52
Q

What is the rate of substitution equation under the rate of neutral molecular evolution

A

X= 2Nu x 1/(2N) = u

53
Q

What does the rate of accumulation of new substitutions per generation depend on

A

The neutral mutation rate and independence of the population size

54
Q

What is K

A

The expected number of substitutions per site between two homologous DNA sequences from two species

55
Q

What is K proportional to

A

The mutation rate

56
Q

What equation is used to estimate K

A

K = D/L
D- the total number of differences
L- the total number of sites considered

57
Q

What does the neutral model predict in terms of time

A

Evolution should be constant over time since it depends only on the neutral mutation rate, u

58
Q

What equation is used to predict mutation rate

A

T= K/ (2U)

59
Q

What can patterns of point mutations be estimated using

A

Nucleotide substitutions

60
Q

What are the feutures of the mammalian mitochondrial genome

A

Circular, double stranded DNA
15- 17 KB in length, 13 protein coding genes, 2 rRNA genes, 22 tRNA genes
A control region

61
Q

What is the relative rate test equation

A

Kxa= Kxb

62
Q

What is the generation time effect hypothesis

A

Errors in DNA replication in germ line cells is a major source of mutation
The hypothesis predicts a higher mutation rate per time unit in species with shorter generation time

63
Q

How much of the human genome encodes for proteins

A

1%

64
Q

How much of the human genome is conserved

A

5%

65
Q

Characteristics of the tripartite motif protein

A

Primate genomes encode for defending themselves against retroviruses

66
Q

What happened with the anti - malarial drug pyrimethamine

A

Introduced in 1970s, resistance spread to fixation in 6 years, it was induced by specific point mutations in active site of parasite

67
Q

Why is population genetics needed?

A

Its not always clear what trait should be measured
We need to rule out chance effect

68
Q

What does Tajimas D do

A

Compares the relative abundance of intermediate and low frequency variatiants

69
Q

What does D< 0 mean

A

An excess of intermediate frequency variants

70
Q

How to make a linkage mapping cross

A
  1. cross the two parental types
  2. Cross the hybrid offspring
  3. Recombination takes place during meiosis, shuffling the parental genomes around
  4. The progeny of F1 cross, inheriting recombined parental genomes
71
Q

How to genotype a mapping cross

A

Place genome markers at regular places across the genome that distinguish two parental types

72
Q

How to determine where the casusative gene is

A

Perform a statistical test at regular intervals along each chromosome to test for an association with the trait

73
Q

Examples of an extended phenotype

A

Innates to the animal e.g. burrowing behaviour of mice

74
Q

What are skyscrapers in manhatton plots

A

Regions with genes that explain variation

75
Q

What is the fixation index

A

The inbreeding in subpopulations (S) is relative to in the total population (T)

76
Q

What did Sewall Wright propose

A

Inbreeding could be used as a measure of differentiation among subpopulations

77
Q

What is the fixation index equation

A

Fst = (Ht- Hs)/Ht
Hs: the average heterozygosity in the subpopulation
H1 is the expected heterozygosity in the total population

78
Q

Whats the scale for FST

A

0-1
O means no differentiation
1 is a fixed differentiation

79
Q

What can we use to predict the gene flow

A

Nm (number of migrants in each generation)

80
Q

How can we sample differentiation of genes

A

Microsatellites, SNPS, Sequencing whole genomes

81
Q

What is involved in microsatellites

A

Repeats of 2-5 base pairs in non coding areas, can be amplified using PCR

82
Q

Disadvantages and advantages with sequencing whole genome

A

More costly, more resolution, can detect bigger mutations

83
Q

Example 1: Arabidopsis lyrate on serpentine soils

A

25 individuals from 4 populations, detected 8.4 million polymorphisms across the genome, 96 had allele frequency differences of greater than 80% between soil types

84
Q

Why do small horns/ scurns persist when they have costs to male reproductive success

A

Horns is determined by many genes of small effect and are just an indicator of quality
Genes associated with small horns confer a fitness advantage in females
Genes associated with samll horns have some other benifit to males

85
Q

What are the two social forms of fire ants

A

Monogynes: single queen
Polygynes: multiple queens that are smaller

86
Q

What are the two different forms of fire ants determined by

A

GP-9 gene

87
Q

What is a super gene

A

A number of tightly linked genes that are not affected by recombination

88
Q

What is cis-regulatory variation

A

Mutations/ regions that occur very close to the gene that the gene is regulating

89
Q

What happens at the promoter of a gene

A

Where transcription is initiated, RNA will bind to that promoter to initiate transcription

90
Q

What do enhancers do

A

Transcription factors bind and interact to the promoter and can be controlled by different enhancers

91
Q

What happens post- transcriptionally

A

Alternative splicing, allows you to alter the sequence of the final protein, can remove exons after transcription or keep them to create different sequences of exons

Biology (9 decks)

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